megpy 1.1.0__tar.gz

megpy-1.1.0/LICENSE

@@ -0,0 +1,165 @@
+                   GNU LESSER GENERAL PUBLIC LICENSE
+                       Version 3, 29 June 2007
+
+ Copyright (C) 2007 Free Software Foundation, Inc. <https://fsf.org/>
+ Everyone is permitted to copy and distribute verbatim copies
+ of this license document, but changing it is not allowed.
+
+
+  This version of the GNU Lesser General Public License incorporates
+the terms and conditions of version 3 of the GNU General Public
+License, supplemented by the additional permissions listed below.
+
+  0. Additional Definitions.
+
+  As used herein, "this License" refers to version 3 of the GNU Lesser
+General Public License, and the "GNU GPL" refers to version 3 of the GNU
+General Public License.
+
+  "The Library" refers to a covered work governed by this License,
+other than an Application or a Combined Work as defined below.
+
+  An "Application" is any work that makes use of an interface provided
+by the Library, but which is not otherwise based on the Library.
+Defining a subclass of a class defined by the Library is deemed a mode
+of using an interface provided by the Library.
+
+  A "Combined Work" is a work produced by combining or linking an
+Application with the Library.  The particular version of the Library
+with which the Combined Work was made is also called the "Linked
+Version".
+
+  The "Minimal Corresponding Source" for a Combined Work means the
+Corresponding Source for the Combined Work, excluding any source code
+for portions of the Combined Work that, considered in isolation, are
+based on the Application, and not on the Linked Version.
+
+  The "Corresponding Application Code" for a Combined Work means the
+object code and/or source code for the Application, including any data
+and utility programs needed for reproducing the Combined Work from the
+Application, but excluding the System Libraries of the Combined Work.
+
+  1. Exception to Section 3 of the GNU GPL.
+
+  You may convey a covered work under sections 3 and 4 of this License
+without being bound by section 3 of the GNU GPL.
+
+  2. Conveying Modified Versions.
+
+  If you modify a copy of the Library, and, in your modifications, a
+facility refers to a function or data to be supplied by an Application
+that uses the facility (other than as an argument passed when the
+facility is invoked), then you may convey a copy of the modified
+version:
+
+   a) under this License, provided that you make a good faith effort to
+   ensure that, in the event an Application does not supply the
+   function or data, the facility still operates, and performs
+   whatever part of its purpose remains meaningful, or
+
+   b) under the GNU GPL, with none of the additional permissions of
+   this License applicable to that copy.
+
+  3. Object Code Incorporating Material from Library Header Files.
+
+  The object code form of an Application may incorporate material from
+a header file that is part of the Library.  You may convey such object
+code under terms of your choice, provided that, if the incorporated
+material is not limited to numerical parameters, data structure
+layouts and accessors, or small macros, inline functions and templates
+(ten or fewer lines in length), you do both of the following:
+
+   a) Give prominent notice with each copy of the object code that the
+   Library is used in it and that the Library and its use are
+   covered by this License.
+
+   b) Accompany the object code with a copy of the GNU GPL and this license
+   document.
+
+  4. Combined Works.
+
+  You may convey a Combined Work under terms of your choice that,
+taken together, effectively do not restrict modification of the
+portions of the Library contained in the Combined Work and reverse
+engineering for debugging such modifications, if you also do each of
+the following:
+
+   a) Give prominent notice with each copy of the Combined Work that
+   the Library is used in it and that the Library and its use are
+   covered by this License.
+
+   b) Accompany the Combined Work with a copy of the GNU GPL and this license
+   document.
+
+   c) For a Combined Work that displays copyright notices during
+   execution, include the copyright notice for the Library among
+   these notices, as well as a reference directing the user to the
+   copies of the GNU GPL and this license document.
+
+   d) Do one of the following:
+
+       0) Convey the Minimal Corresponding Source under the terms of this
+       License, and the Corresponding Application Code in a form
+       suitable for, and under terms that permit, the user to
+       recombine or relink the Application with a modified version of
+       the Linked Version to produce a modified Combined Work, in the
+       manner specified by section 6 of the GNU GPL for conveying
+       Corresponding Source.
+
+       1) Use a suitable shared library mechanism for linking with the
+       Library.  A suitable mechanism is one that (a) uses at run time
+       a copy of the Library already present on the user's computer
+       system, and (b) will operate properly with a modified version
+       of the Library that is interface-compatible with the Linked
+       Version.
+
+   e) Provide Installation Information, but only if you would otherwise
+   be required to provide such information under section 6 of the
+   GNU GPL, and only to the extent that such information is
+   necessary to install and execute a modified version of the
+   Combined Work produced by recombining or relinking the
+   Application with a modified version of the Linked Version. (If
+   you use option 4d0, the Installation Information must accompany
+   the Minimal Corresponding Source and Corresponding Application
+   Code. If you use option 4d1, you must provide the Installation
+   Information in the manner specified by section 6 of the GNU GPL
+   for conveying Corresponding Source.)
+
+  5. Combined Libraries.
+
+  You may place library facilities that are a work based on the
+Library side by side in a single library together with other library
+facilities that are not Applications and are not covered by this
+License, and convey such a combined library under terms of your
+choice, if you do both of the following:
+
+   a) Accompany the combined library with a copy of the same work based
+   on the Library, uncombined with any other library facilities,
+   conveyed under the terms of this License.
+
+   b) Give prominent notice with the combined library that part of it
+   is a work based on the Library, and explaining where to find the
+   accompanying uncombined form of the same work.
+
+  6. Revised Versions of the GNU Lesser General Public License.
+
+  The Free Software Foundation may publish revised and/or new versions
+of the GNU Lesser General Public License from time to time. Such new
+versions will be similar in spirit to the present version, but may
+differ in detail to address new problems or concerns.
+
+  Each version is given a distinguishing version number. If the
+Library as you received it specifies that a certain numbered version
+of the GNU Lesser General Public License "or any later version"
+applies to it, you have the option of following the terms and
+conditions either of that published version or of any later version
+published by the Free Software Foundation. If the Library as you
+received it does not specify a version number of the GNU Lesser
+General Public License, you may choose any version of the GNU Lesser
+General Public License ever published by the Free Software Foundation.
+
+  If the Library as you received it specifies that a proxy can decide
+whether future versions of the GNU Lesser General Public License shall
+apply, that proxy's public statement of acceptance of any version is
+permanent authorization for you to choose that version for the
+Library.

megpy-1.1.0/PKG-INFO

@@ -0,0 +1,71 @@
+Metadata-Version: 2.1
+Name: megpy
+Version: 1.1.0
+Summary: MEGPy
+Home-page: https://www.github.com/gsnoep/megpy
+Author: Garud Snoep
+Keywords: fusion simulation toolkit
+Classifier: Programming Language :: Python :: 3
+Classifier: Operating System :: OS Independent
+Description-Content-Type: text/markdown
+License-File: LICENSE
+
+# MEGPy: Magnetic Equilibrium Geometry Python
+MEGPy is a package for quick **extraction of (local) equilibrium quantities** and visualisation of 2D magnetic equilibria used in magnetic confinement fusion research.
+It offers both a command line interface (CLI) and Python API.
+
+# Getting started
+To get MEGPy clone and install the latest version:
+```bash
+$ git clone git@github.com:gsnoep/megpy.git
+$ cd megpy
+$ pip install --user -e .
+```
+
+To use MEGPy call the CLI:
+```bash
+$ python -m megpy <file_path> <parameterization> <x_fs>
+```
+For details on the CLI options:
+```bash
+$ python -m megpy -h
+```
+Or use the Python API, of which some examples can be found in /examples/.
+
+Join the repository to contribute or raise issues!
+
+# Supported equilibrium formats
+- EQDSK [(g-file)](https://w3.pppl.gov/ntcc/TORAY/G_EQDSK.pdf) from EFIT, ESCO, CHEASE or LIUQE
+
+To be added:
+- IMAS equilibrium IDS
+
+# Supported flux-surface geometries
+- Miller [(doi)](https://doi.org/10.1063/1.872666)
+- Turnbull-Miller [(doi)](https://doi.org/10.1063/1.873380)
+- Fourier / generalised Miller [(doi)](https://doi.org/10.1088/0741-3335/51/10/105009)
+- Miller eXtended Harmonic (MXH) [(doi)](https://doi.org/10.1088/1361-6587/abc63b)
+
+# Citation
+If you use MEGPy in your research, please cite [(bibtex)](https://github.com/gsnoep/megpy/blob/main/citation.bib):
+>G. Snoep, J.T.W. Koenders, C. Bourdelle, J. Citrin and JET contributors, "Improved flux-surface parameterization through constrained nonlinear optimization," _Physics of Plasmas_ **30**, 063906 (2023)
+
+
+                    .#&%%%-.
+                <===#%%%%%%%%%%.
+                   ?==%%( )%%%%%
+                    )%%%%%%%%%%%%\
+                    )%%%%%%%%%%%..%%%
+                    )%%%%%%%%&..    .\%.
+                     %%%%%%%% &\,.  ..\%.
+                     M%%%%%%%...&&%\%%%%%%%%%-
+                       %%%%%.       .\%%%%%%%%%%.
+                        %%%..             .\%%%%%%%.
+                         E...               .\%%%%%%%-.
+                            &...              )%%%%(%%%.
+                               G..   .&).     )GS\   \%%%%%%-.
+                                  \&))  \&(%^^          \&%%%%%&.
+                                   )%%    %%                 \%%%%%%%&.
+                                .&&     .%                        \&\\%%%%\\&..
+                             .%<       (\                               %    \
+                      .::-P-..-&  &&-Y&--.

megpy-1.1.0/README.md

@@ -0,0 +1,59 @@
+# MEGPy: Magnetic Equilibrium Geometry Python
+MEGPy is a package for quick **extraction of (local) equilibrium quantities** and visualisation of 2D magnetic equilibria used in magnetic confinement fusion research.
+It offers both a command line interface (CLI) and Python API.
+
+# Getting started
+To get MEGPy clone and install the latest version:
+```bash
+$ git clone git@github.com:gsnoep/megpy.git
+$ cd megpy
+$ pip install --user -e .
+```
+
+To use MEGPy call the CLI:
+```bash
+$ python -m megpy <file_path> <parameterization> <x_fs>
+```
+For details on the CLI options:
+```bash
+$ python -m megpy -h
+```
+Or use the Python API, of which some examples can be found in /examples/.
+
+Join the repository to contribute or raise issues!
+
+# Supported equilibrium formats
+- EQDSK [(g-file)](https://w3.pppl.gov/ntcc/TORAY/G_EQDSK.pdf) from EFIT, ESCO, CHEASE or LIUQE
+
+To be added:
+- IMAS equilibrium IDS
+
+# Supported flux-surface geometries
+- Miller [(doi)](https://doi.org/10.1063/1.872666)
+- Turnbull-Miller [(doi)](https://doi.org/10.1063/1.873380)
+- Fourier / generalised Miller [(doi)](https://doi.org/10.1088/0741-3335/51/10/105009)
+- Miller eXtended Harmonic (MXH) [(doi)](https://doi.org/10.1088/1361-6587/abc63b)
+
+# Citation
+If you use MEGPy in your research, please cite [(bibtex)](https://github.com/gsnoep/megpy/blob/main/citation.bib):
+>G. Snoep, J.T.W. Koenders, C. Bourdelle, J. Citrin and JET contributors, "Improved flux-surface parameterization through constrained nonlinear optimization," _Physics of Plasmas_ **30**, 063906 (2023)
+
+
+                    .#&%%%-.
+                <===#%%%%%%%%%%.
+                   ?==%%( )%%%%%
+                    )%%%%%%%%%%%%\
+                    )%%%%%%%%%%%..%%%
+                    )%%%%%%%%&..    .\%.
+                     %%%%%%%% &\,.  ..\%.
+                     M%%%%%%%...&&%\%%%%%%%%%-
+                       %%%%%.       .\%%%%%%%%%%.
+                        %%%..             .\%%%%%%%.
+                         E...               .\%%%%%%%-.
+                            &...              )%%%%(%%%.
+                               G..   .&).     )GS\   \%%%%%%-.
+                                  \&))  \&(%^^          \&%%%%%&.
+                                   )%%    %%                 \%%%%%%%&.
+                                .&&     .%                        \&\\%%%%\\&..
+                             .%<       (\                               %    \
+                      .::-P-..-&  &&-Y&--.

megpy-1.1.0/megpy/__init__.py

@@ -0,0 +1,24 @@
+import sys
+from pkg_resources import (
+    DistributionNotFound as _DistributionNotFound,
+    get_distribution as _get_distribution,
+)
+
+if sys.version_info < (3,7):
+    raise Exception("MEGPy does not support Python < 3.7")
+
+from .equilibrium import Equilibrium
+from .localequilibrium import LocalEquilibrium
+from .tracer import *
+
+
+__all__= [
+    "Equilibrium",
+    "LocalEquilibrium"
+]
+
+try:
+    _distribution = _get_distribution("megpy")
+    __version__ = _distribution.version
+except _DistributionNotFound:
+    __version__ = "unknown"

megpy-1.1.0/megpy/__main__.py

@@ -0,0 +1,4 @@
+from .cli import parse
+
+if __name__ == "__main__":
+    parse()

megpy-1.1.0/megpy/cli.py

@@ -0,0 +1,92 @@
+import os
+import argparse
+
+from .equilibrium import Equilibrium
+from .localequilibrium import LocalEquilibrium
+from .utils import *
+
+def is_valid_file(file):
+    if not os.path.exists(file):
+        raise argparse.ArgumentTypeError('The provided path {} does not lead to an existing EQDSK file, check input!'.format(file))
+    else:
+        return file
+
+def str2bool(v):
+    if isinstance(v, bool):
+        return v
+    if v.lower() in ('yes', 'true', 't', 'y', '1'):
+        return True
+    elif v.lower() in ('no', 'false', 'f', 'n', '0'):
+        return False
+    else:
+        raise argparse.ArgumentTypeError('Boolean value expected.')
+
+def parse():
+    parser = argparse.ArgumentParser(description='MEGPy: Extract flux surface shaping parameters (Miller, Turnbull-Miller, etc) from EQDSK files.')
+    parser.add_argument(dest='file', type=is_valid_file, help='valid path to an EQDSK file', metavar='FILE')
+    parser.add_argument(dest='method', type=str, default='turnbull', help='parameterization to be used for fitting the flux surfaces and Bpol', metavar='PARAM')
+    parser.add_argument(dest='x_fs', type=float, help='radial location to extract flux surface and Bpol shaping parameters', metavar='POSITION')
+    parser.add_argument('-x', '--x_label', dest='x_label', required=False, type=str, default='rho_tor', help='label of the radial location (e.g. rho_tor, rho_pol, r/a)', metavar='STR')
+    parser.add_argument('-r', '--refine', dest='refine', required=False, type=int, default=0, help='refine the poloidal flux map psi(R,Z) <r> times', metavar='INT')
+    parser.add_argument('--n_x', dest='n_x', required=False, type=int, default=9, help='number of radial points used for radial derivatives', metavar='INT')
+    parser.add_argument('--n_theta', dest='n_theta', required=False, type=int, default=7200, help='number of poloidal grid points', metavar='INT')
+    parser.add_argument('--n_harmonics', dest='n_harmonics', required=False, type=int, default=3, help='number of harmonics used in the optimization for fourier/miller_general/mxh', metavar='INT')
+    parser.add_argument('-p', '--printer', dest='printer', required=False, type=str, default='GENE', help='name of the code to print the geometry input values for', metavar='STR')
+    parser.add_argument('--printer_lref', dest='lref', required=False, type=str, default='a', help='reference length Lref used to normalized code input values', metavar='STR')
+    parser.add_argument('-a', '--analytic-geo', dest='analytic_geo', required=False, nargs='?', const=True, default=True, type=str2bool, help='include the analytical Miller parameters for comparison y/n', metavar='BOOL')
+    parser.add_argument('--opt-bpol', dest='opt_bpol', required=False, nargs='?', const=False, default=False, type=str2bool, help='optimize shape derivative parameters by minimizing the error in Bpol', metavar='BOOL')
+    parser.add_argument('--opt-deriv', dest='opt_deriv', required=False, nargs='?', const=False, default=False, type=str2bool, help='optimize shape derivative parameters by minimizing the error in dRdr, dZdr, dRdtheta, dZdtheta', metavar='BOOL')
+    args = parser.parse_args()
+
+    eq = Equilibrium()
+    eq.read_geqdsk(f_path=args.file)
+    if args.refine > 1:
+        eq.add_derived(refine=args.refine)
+    else:
+        eq.add_derived()
+    if args.x_label == 'r/a':
+        print('Processing Equilibrium to determine r/a(psi)...')
+        eq.add_fluxsurfaces()
+
+    locgeo = LocalEquilibrium(args.method,
+                              eq,
+                              args.x_fs,
+                              x_label=args.x_label,
+                              n_x=args.n_x,
+                              n_theta=args.n_theta,
+                              n_harmonics=args.n_harmonics,
+                              analytic_shape=args.analytic_geo,
+                              opt_bpol=args.opt_bpol,
+                              opt_deriv=args.opt_deriv,
+                              diag_lsq=0,
+                              verbose=True)
+    
+    
+    if args.printer:
+        locgeo.printer(args.printer,locgeo.shape,locgeo.param_labels,locgeo.shape_deriv,locgeo.deriv_labels)
+        #if incl_analytic_geo:
+        #    self.printer(printer,self.shape_analytic,self.param_labels,self.shape_deriv_analytic,self.deriv_labels)
+        
+    #if not args.no_plots:
+    #    locgeo.plot_all(incl_analytic_geo=args.analytic_geo,opt_bpol=args.opt_bpol)
+
+
+
+str_megpy=["\n                    .#&%%%-.\n"
+          ,"                <===#%%%%%%%%%%.\n"
+          ,"                   ?==%%( )%%%%\\\n"
+          ,"                    )%%%%%%%%%%%%\\\n"
+          ,"                    )%%%%%%%%%%%..%%%\n"
+          ,"                    )%%%%%%%%&..    .\%.\n"
+          ,"                     %%%%%%%% &\,.  ...\\%.\n"
+          ,"                     M%%%%%%%...&&%\%%%%%%%%%-\n"
+          ,"                       %%%%%.       .\%%%%%%%%%%.\n"
+          ,"                        %%%..             .\%%%%%%%.\n"
+          ,"                         E...               .\%%%%%%%-.\n"
+          ,"                            &...              )%%%%(%%%.\n"
+          ,"                               G..   .&).     )GS\   \%%%%%%-\n"
+          ,"                                  \&))  \&(%^^          \&%%%%%&.\n"
+          ,"                                   )%%    %%                 \%%%%%%%&.\n"
+          ,"                                .&&     .%                        \&\\%%%%\\&..\n"
+          ,"                             .%<       (\                               %   \\\n"
+          ,"                      .::-P-..-&  &&-Y&--.\n\n"]